title: Deep transcriptome sequencing of rhizome and aerial-shoot in Sorghum propinquum.
abstract: Transcriptomic data for Sorghum propinquum, the wild-type sorghum, are limited in public databases. S. propinquum has a subterranean rhizome and transcriptome data will help in understanding the molecular mechanisms underlying rhizome formation. We sequenced the transcriptome of S. propinquum aerial-shoot and rhizome using an Illumina platform. More than 70 % of the genes in the S. propinquum genome were expressed in aerial-shoot and rhizome. The expression patterns of 1963 and 599 genes, including transcription factors, were specific or enriched in aerial-shoot and rhizome respectively, indicating their possible roles in physiological processes in these tissues. Comparative analysis revealed several cis-elements, ACGT box, GCCAC, GATC and TGACG box, which showed significantly higher abundance in aerial-shoot-specific genes. In rhizome-specific genes MYB and ROOTMOTIFTAPOX1 motifs, and 10 promoter and cytokinin-responsive elements were highly enriched. Of the S. propinquum genes, 27.9 % were identified as alternatively spliced and about 60 % of the alternative splicing (AS) events were tissue-specific, suggesting that AS played a crucial role in determining tissue-specific cellular function. The transcriptome data, especially the co-localized rhizome-enriched expressed transcripts that mapped to the publicly available rhizome-related quantitative trait loci, will contribute to gene discovery in S. propinquum and to functional studies of the sorghum genome. Deep transcriptome sequencing revealed a clear difference in the expression patterns of genes between aerial-shoot and rhizome in S. propinquum. This data set provides essential information for future studies into the molecular genetic mechanisms involved in rhizome formation.
authors.affiliation: Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun St., Beijing, 100081, China.
authors.forename: Ting
authors.initials: T
authors.lastname: Zhang
authors.forename: Xiuqin
authors.initials: X
authors.lastname: Zhao
authors.forename: Wensheng
authors.initials: W
authors.lastname: Wang
authors.forename: Liyu
authors.initials: L
authors.lastname: Huang
authors.forename: Xiaoyue
authors.initials: X
authors.lastname: Liu
authors.forename: Ying
authors.initials: Y
authors.lastname: Zong
authors.forename: Linghua
authors.initials: L
authors.lastname: Zhu
authors.forename: Daichang
authors.initials: D
authors.lastname: Yang
authors.forename: Binying
authors.initials: B
authors.lastname: Fu
authors.forename: Zhikang
authors.initials: Z
authors.lastname: Li
mesh_terms: D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D035261:Plant Components, Aerial / Q000378:metabolism*; D018749:RNA, Plant / Q000302:isolation & purification; D060888:Real-Time Polymerase Chain Reaction; D027343:Rhizome / Q000378:metabolism*; D045868:Sorghum / Q000235:genetics*; D059467:Transcriptome
chemical_list: D018749:RNA, Plant